The present study aims to investigate the effects of Phragmites communis and Zizania aquatica on rhizosphere soil enzyme activity and bacterial community structure in a surface flow constructed wetland (SFCW) for the treatment of domestic sewage from the Shanxi province of China. The basic physical and chemical properties of the soil, the contents of soil urease (UE), alkaline phosphatase (ALP), soil microbial biomass carbon and nitrogen (SMBC, SMBN), and bacterial community structure were measured in the Phragmites communis group (PG), Zizania aquatica group (ZG), and control group (CG), respectively. The results showed that (1) the contents of UE, ALP, SMBC, and SMBN in rhizosphere soil of PG were more than those of ZG; (2) the highest bacterial abundance and αdiversity appeared in PG, in which Gp6 was the most abundant bacterial genus in PG; (3) the main functions of the dominant bacteria Gp6 and Longilinea in PG were involved in metabolizing multiple carbohydrates and participating in the carbon cycle in the soil based on the clusters of orthologous groups pathway analysis data; (4) the bacterial community of PG was mainly affected by the positive correlation with arsenic, nickel, or SMBC via the redundancy analysis. Collectively, Phragmites communis is a recommended species for wastewater wetland treatment system in Shanxi province, and the special enzymes and dominant bacteria in plant rhizosphere soil had obvious functions of removing organic pollutants. Besides, the influences of environmental factors on rhizosphere bacteria and the combined effects of Phragmites communis and dominant bacteria in wetland wastewater treatment system should be taken seriously.